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Current opinion in structural biology最新文献

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Transformers as a substrate for structural biology 变压器作为结构生物学的基质。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-04-01 Epub Date: 2026-02-06 DOI: 10.1016/j.sbi.2025.103218
Ashar J. Malik , Stephanie Portelli , David B. Ascher
Transformers are rapidly reshaping structural biology. We argue the reason is “Emergent Latent Biology” (ELB): transformers place proteins into high-dimensional representations where hidden biophysical patterns become easier to see. We explore this concept across four key areas: protein folding, variant effects, protein–protein and protein–drug interactions. Highlighting recent gains, we note that traditional, physics-based calculations are still required for the hardest quantitative jobs, like predicting precise binding strength. Furthermore, we draw attention to major pitfalls, arguing progress depends on solving the critical “chemistry gap,” modelling chemical modifications, and the “dynamics gap”, predicting protein movement, which requires better validation methods and new large-scale experiments.
变形金刚正在迅速重塑结构生物学。我们认为原因是“涌现的潜在生物学”(ELB):变形器将蛋白质放入高维表示中,隐藏的生物物理模式变得更容易看到。我们在四个关键领域探索这一概念:蛋白质折叠、变异效应、蛋白质-蛋白质和蛋白质-药物相互作用。强调最近的进展,我们注意到传统的,基于物理的计算仍然需要最困难的定量工作,如预测精确的结合强度。此外,我们提请注意主要缺陷,认为进展取决于解决关键的“化学差距”,模拟化学修饰和“动力学差距”,预测蛋白质运动,这需要更好的验证方法和新的大规模实验。
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引用次数: 0
Why are there no clinically-approved drugs targeting disordered proteins? 为什么没有临床批准的针对无序蛋白质的药物?
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-04-01 Epub Date: 2026-03-02 DOI: 10.1016/j.sbi.2026.103236
Thomas Löhr , Gogulan Karunanithy , Gabriella T. Heller
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are critical regulators in health and disease but remain underexploited as drug targets. Unlike folded proteins, they populate dynamic ensembles where interactions can be transient or multivalent, and both enthalpic and entropic contributions shape binding, complicating ligand discovery. Here, we analyze three key barriers hindering progress: (1) nontraditional binding mechanisms that challenge classical drug design, (2) experimental and computational limitations for studying disorder, and (3) a lack of systematic datasets. Our analysis of the Biological Magnetic Resonance Data Bank (BMRB) and BindingDB highlights the extreme underrepresentation of IDPs and IDRs, underscoring the need for community-driven data resources. By integrating new binding paradigms, tailored methodologies, and standardized datasets, drug discovery can begin to harness IDPs as a new therapeutic frontier.
内在无序蛋白(IDPs)和内在无序区(IDRs)是健康和疾病的关键调节因子,但作为药物靶点尚未得到充分利用。与折叠的蛋白质不同,它们填充动态集成,其中相互作用可以是短暂的或多价的,并且焓和熵的贡献都形成了结合,使配体的发现变得复杂。在此,我们分析了阻碍进展的三个关键障碍:(1)挑战经典药物设计的非传统结合机制;(2)研究疾病的实验和计算限制;(3)缺乏系统的数据集。我们对生物磁共振数据库(BMRB)和BindingDB的分析强调了IDPs和idr的极度代表性不足,强调了对社区驱动数据资源的需求。通过整合新的结合范例、量身定制的方法和标准化的数据集,药物发现可以开始利用国内流离失所者作为新的治疗前沿。
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引用次数: 0
In situ structural studies of membrane protein megacomplexes 膜蛋白巨复合体的原位结构研究
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-04-01 Epub Date: 2026-02-12 DOI: 10.1016/j.sbi.2026.103222
Shan Sun, Sen-Fang Sui
Membrane protein complexes are essential for cellular functions, which rely on both constituent protein structures and their interactions within native membranes. While in vitro methods have successfully yielded high-resolution structures of individual proteins and subcomplexes, these approaches typically require detergent extraction and extensive purification, which can disrupt the native membrane environment and potentially alter the supramolecular organization. In situ structural biology has therefore emerged as an effective strategy to overcome these limitations by directly visualizing macromolecular machines within their physiological context. With continuous technological advancements, several recent studies have resolved in situ structures of large protein complexes at high or even near-atomic resolution. This review focuses on recent in situ high-resolution studies of membrane protein megacomplexes, highlighting key technical innovations, structural insights, and the remaining challenges and opportunities in the field.
膜蛋白复合物是细胞功能所必需的,它依赖于组成蛋白结构和它们在天然膜内的相互作用。虽然体外方法已经成功地获得了单个蛋白质和亚复合物的高分辨率结构,但这些方法通常需要洗涤剂提取和大量纯化,这可能会破坏天然膜环境,并可能改变超分子组织。因此,原位结构生物学已经成为克服这些限制的有效策略,通过在其生理背景下直接可视化大分子机器。随着技术的不断进步,最近的一些研究已经在高甚至近原子分辨率下解决了大型蛋白质复合物的原位结构。本文综述了近年来膜蛋白巨复合物的原位高分辨率研究,重点介绍了该领域的关键技术创新、结构见解以及存在的挑战和机遇。
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引用次数: 0
Rational protein design 合理的蛋白质设计
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-04-01 Epub Date: 2026-02-12 DOI: 10.1016/j.sbi.2026.103224
Joel J. Chubb , Aimee L. Boyle , Katherine I. Albanese
Protein design enables the creation of novel structures and functions beyond those found in nature, with recent progress accelerated by computational modeling and machine learning. However, many automated methods act as black boxes, limiting mechanistic insight. Here we highlight the continuing importance of rational protein design, defined as an approach rooted in physical principles, chemical intuition, and sequence–structure–function relationships. We outline three complementary strategies: backbone-first, sequence-first, and function-first, which provide interpretable design frameworks and enable robust scaffold generation, motif incorporation, and functional engineering. Looking forward, we argue that hybrid workflows combining rational principles with machine learning offer the most promising route to dynamic, explainable, and generalizable protein design.
蛋白质设计能够创造出超越自然界的新结构和功能,最近的进展通过计算建模和机器学习加速。然而,许多自动化方法就像黑盒一样,限制了机械的洞察力。在这里,我们强调了理性蛋白质设计的持续重要性,它被定义为一种根植于物理原理、化学直觉和序列-结构-功能关系的方法。我们概述了三种互补的策略:骨干优先、序列优先和功能优先,它们提供了可解释的设计框架,并使强大的支架生成、基序整合和功能工程成为可能。展望未来,我们认为将理性原则与机器学习相结合的混合工作流程为动态、可解释和可推广的蛋白质设计提供了最有希望的途径。
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引用次数: 0
Moving the antibody: Molecular dynamics for molecular mechanisms and developability 移动抗体:分子动力学的分子机制和可展性。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-04-01 Epub Date: 2026-02-18 DOI: 10.1016/j.sbi.2026.103225
Matteo Cagiada , Charlotte M. Deane
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引用次数: 0
Drug–target residence time: Analyzing cooperativity effects in G protein-coupled receptors by mathematical modeling and molecular dynamics simulations 药物靶停留时间:用数学模型和分子动力学模拟分析G蛋白偶联受体的协同效应。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-04-01 Epub Date: 2026-02-07 DOI: 10.1016/j.sbi.2025.103214
Antonio J. Ortiz , Antoniel A.S. Gomes , Pedro Renault , David Romero , Antoni Guillamon , Jesús Giraldo
Drug–target residence time (τ) is reviewed from two perspectives: mathematics and molecular dynamics. The first focuses on the quantification of τ using a mathematical formalism applicable to different pharmacological mechanistic conditions. This formalism is based on the concept of the smallest-modulus eigenvalue of a subsystem of interest, in which the global formation process has been eliminated. The second includes relevant studies of recent years to provide a structural explanation of τ predictions. Special attention is paid to physically supported artificial intelligence methods. The main objective of this minireview is to promote a combined approach in which mathematics and physics work synergistically to describe the complexity associated with τ in G protein-coupled receptors.
从数学和分子动力学两方面对药物靶点停留时间(τ)进行了综述。第一个重点是使用适用于不同药理机制条件的数学形式来量化τ。这种形式基于感兴趣的子系统的最小模特征值的概念,其中消除了全局形成过程。第二部分包括近年来的相关研究,以提供τ预测的结构解释。特别关注物理支持的人工智能方法。这篇综述的主要目的是促进数学和物理协同工作的结合方法,以描述与G蛋白偶联受体τ相关的复杂性。
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引用次数: 0
Machine learning, docking, or physics for structure prediction of ligand-induced ternary complexes 用于配体诱导三元配合物结构预测的机器学习、对接或物理
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-04-01 Epub Date: 2026-01-30 DOI: 10.1016/j.sbi.2025.103217
Riccardo Solazzo , Shu-Yu Chen , Sereina Riniker
Proteolysis-targeting chimeras (PROTACs) and molecular glues promote targeted protein degradation by recruiting an E3 ligase to proteins of interest (POIs). An accurate 3D structure of the ternary complex formed by E3 ligase, ligand, and POI is central to the rational design of degraders. Elucidating this structure with crystallography or cryo-EM can be challenging due to conformational flexibility, dynamic protein-protein interactions, and high-dimensional binding landscapes. To facilitate structure-based design in the absence of an experimental structure, computational approaches have been proposed: (i) multistep methods involving traditional docking pipelines, and (ii) single-step methods with deep learning models to directly predict the complex structure. Multistep methods are limited by sampling complexity, accurate input structures, scoring accuracy, and computational cost, while single-step methods are faster but are constrained by training-data scarcity. Here, we examine recent advances and emerging tools in modeling ternary complexes, critically discuss their predictive power and limitations, and highlight remaining challenges.
靶向蛋白水解嵌合体(PROTACs)和分子胶通过招募E3连接酶到目标蛋白(POIs)上来促进靶向蛋白降解。由E3连接酶、配体和POI组成的三元配合物的精确三维结构是合理设计降解物的关键。由于构象灵活性、动态蛋白质-蛋白质相互作用和高维结合景观,用晶体学或冷冻电镜来阐明这种结构可能具有挑战性。为了在没有实验结构的情况下促进基于结构的设计,已经提出了计算方法:(i)涉及传统对接管道的多步骤方法,以及(ii)使用深度学习模型的单步骤方法直接预测复杂结构。多步方法受到采样复杂性、准确的输入结构、评分准确性和计算成本的限制,而单步方法速度更快,但受到训练数据稀缺性的限制。在这里,我们研究了三元配合物建模的最新进展和新兴工具,批判性地讨论了它们的预测能力和局限性,并强调了仍然存在的挑战。
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引用次数: 0
From sequence to structure: A comprehensive review of deep learning models for RNA structure prediction 从序列到结构:RNA结构预测的深度学习模型的全面回顾。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-04-01 Epub Date: 2026-02-05 DOI: 10.1016/j.sbi.2025.103216
Utkarsh Upadhyay, Anton Dorn, Christian Faber, Alexander Schug
RNA structure prediction remains one of the most challenging problems in computational biology, with significant implications for understanding gene regulation, drug design, and synthetic biology. While deep learning has revolutionized protein structure prediction, RNA presents unique challenges including limited training data, complex noncanonical interactions, and conformational flexibility. This review examines the evolution from traditional physics-based methods to current deep learning approaches for RNA secondary and tertiary structure prediction. After briefly exploring traditional methods, like Direct Coupling Analysis and physics-based simulations, we systematically review three deep learning paradigms: language model–based methods, end-to-end structure predictors, and geometry-distance prediction approaches. Furthermore, we identify critical future research directions focusing on advanced tokenization strategies to address data scarcity and explainable artificial intelligence techniques to improve model interpretability. Despite significant progress, achieving transformative performance requires continued methodological innovation, specifically designed for RNA’s unique characteristics, and a substantial expansion of high-quality structural datasets.
RNA结构预测仍然是计算生物学中最具挑战性的问题之一,对理解基因调控、药物设计和合成生物学具有重要意义。虽然深度学习已经彻底改变了蛋白质结构预测,但RNA面临着独特的挑战,包括有限的训练数据、复杂的非规范相互作用和构象灵活性。本文综述了从传统的基于物理的方法到当前用于RNA二级和三级结构预测的深度学习方法的演变。在简要探讨了传统方法(如直接耦合分析和基于物理的模拟)之后,我们系统地回顾了三种深度学习范式:基于语言模型的方法、端到端结构预测器和几何距离预测方法。此外,我们确定了关键的未来研究方向,重点是先进的标记化策略,以解决数据稀缺性和可解释的人工智能技术,以提高模型的可解释性。尽管取得了重大进展,但实现变革性性能需要持续的方法创新,特别是针对RNA的独特特征设计的方法创新,以及高质量结构数据集的大量扩展。
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引用次数: 0
Ligand-like lipid interactions with membrane proteins: Simulations and machine learning 配体样脂质与膜蛋白的相互作用:模拟和机器学习。
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-04-01 Epub Date: 2026-02-19 DOI: 10.1016/j.sbi.2026.103226
George Hedger , Edward Lyman , Sarah L. Rouse
Membrane lipids can bind to specific sites on membrane proteins in a ligand-like manner and modulate protein structure and function. Molecular dynamics simulations encompass a suite of approaches to identify, characterise, and explain the atomic-level mechanisms that underlie the functional effects of ligand-like lipids on membrane proteins. Simulations have shown good agreement with available structural data on lipid-protein interactions. Building on successes, simulations are now used to identify new interactions and mechanisms de novo for a given membrane protein. In this age of abundance, it is increasingly possible to analyse patterns across large groups of proteins and in ever more complex membrane environments. The dawn of machine learning approaches in lipid-protein cofolding holds considerable promise to synergistically capitalise on this availability of simulation data and uncover new facets of ligand-like lipid biology.
膜脂能以配体样方式结合到膜蛋白上的特定位点,调节蛋白的结构和功能。分子动力学模拟包含了一套方法来识别、表征和解释配体样脂质对膜蛋白的功能作用的原子水平机制。模拟结果与现有的脂质-蛋白相互作用结构数据一致。在成功的基础上,模拟现在用于确定新的相互作用和机制,为一个给定的膜蛋白从头开始。在这个物质丰富的时代,越来越有可能在更复杂的膜环境中分析大量蛋白质的模式。脂质-蛋白共折叠中机器学习方法的曙光为协同利用这种模拟数据的可用性和揭示配体样脂质生物学的新方面带来了相当大的希望。
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引用次数: 0
Altered residence time as a cause of drug resistance 滞留时间的改变是抗药性的原因
IF 6.1 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-04-01 Epub Date: 2026-02-12 DOI: 10.1016/j.sbi.2026.103219
Brian M. Farrell , Markus A. Seeliger
Drug-target residence time is a crucial determinant of pharmacological efficacy, complementing traditional equilibrium affinity measures. Variations in residence time influence drug selectivity, therapeutic windows, and resistance development, yet its molecular underpinnings remain incompletely understood. Here we review factors governing residence time, including kinetic parameters and structural influences, and examine how mutations can alter dissociation rates to confer drug resistance. We highlight recent advances in experimental and computational methods, such as molecular dynamics simulations, that enable prediction and rational design of compounds with optimized residence times. These insights underscore the importance of incorporating kinetic considerations into drug discovery to improve efficacy and overcome resistance. Our findings suggest that optimizing residence time offers a promising strategy to enhance therapeutic outcomes for diverse diseases.
药物靶点停留时间是药理学疗效的关键决定因素,补充了传统的平衡亲和力措施。停留时间的变化影响药物选择性、治疗窗口和耐药性的发展,但其分子基础仍不完全清楚。在这里,我们回顾了控制停留时间的因素,包括动力学参数和结构影响,并研究了突变如何改变解离速率以赋予耐药性。我们强调了实验和计算方法的最新进展,例如分子动力学模拟,可以预测和合理设计具有优化停留时间的化合物。这些见解强调了将动力学考虑纳入药物发现以提高疗效和克服耐药性的重要性。我们的研究结果表明,优化停留时间为提高各种疾病的治疗效果提供了一个有希望的策略。
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引用次数: 0
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Current opinion in structural biology
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